Functional Impact of Glycans and their Curation

From GlyGen Wiki
(Redirected from BioCuration Workshop 2023)
Jump to navigation Jump to search

There will be two glycan function events in Padua, Italy. We encourage everyone who is attending the Sunday pre-workshop to also join us Monday, if they plan to stay for the conference:

All Day Pre-Workshop

Sunday April 23, 2023, 9:00am - 5:00pm

Hotel NH Padova, Padua, Italy


This event is separate from the 2023 Biocuration Conference.

2-Hour Biocuration Workshop

Monday April 24, 2023, 11:00am - 1:00pm

Cultural Center Altinate San Gaetano, Padua, Italy


This event is hosted by the 2023 Biocuration Conference.


Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information such as MIM, Monarch Initiative, UniProt, and Genomics England, and others focus primarily on the macromolecules within the central dogma of molecular biology (DNA, RNA, proteins). In order to gain a more complete understanding of human disease, there is a need to capture the functional impact of glycans and glycosylation on biological processes. While the aforementioned resources include glycan-related genes, such as biosynthetic and degradative enzymes, the function and disease annotations are usually associated with the gene product rather than with the relevant glycosylation and glycan structural changes. Expression of glycan-related genes represents only a subset of factors affecting protein glycosylation. The functional impact of a specific glycan structure may depend on the protein to which it is bound, site of attachment, truncation or loss of the entire glycan structure. A catalog of glycosylation combinations, their relationship with other biomolecules, and their functional implications will provide insight into the biological roles of glycans and the impact of genetic and environmental factors on their expression. The purpose of this workshop is to bring together subject matter experts, tool developers and biocurators from resources that annotate content that is related to the functional impact of glycans. Each resource will do a short presentation on their data of interest, including  types of annotations, what impact glycan function might have on these annotations, and standards and ontologies they are using. This will be followed by a jamboree/hackathon where we will discuss selected publications to identify commonalities and gaps in our current curation practices, and provide potential solutions. The attendees will help identify areas where curators, data wranglers, and text mining experts can collaborate to address gaps in glycan and glycosylation annotations, leverage each other’s work to improve their respective resources and encourage data sharing amongst resources.

Organization Committee

Raja Mazumder (GlySpace, GlyGen), Mike Tiemeyer (GlySpace, GlyGen), Rene Ranzinger (GlyGen), Karina Martinez (GlyGen), Jeet Vora (GlyGen), Maria Martin (UniProt, GlyGen), Kiyoko Aoki-Kinoshita (GlySpace, GlyCosmos, GlyTouCan), Frederique Lisacek (GlySpace, GlyConnect), Cecilia Arighi (PIR, BioCreative, UniProt), Randi Vita (IEDB)

All Day Pre-Workshop (Sunday April 23)

GlyGen and the Society for Glycobiology are sponsoring a special pre-workshop prior to the 2023 International Biocuration Conference in Padua, Italy. The purpose of this workshop is to focus on community building and learning what each resource is doing related to the functional impact of glycans.


Hotel NH Padova, Via Niccolò Tommaseo, 61, 35131 Padova, Italy

16 minute walking time to Centro Culturale San Gaetano (Conference venue)

Getting there

From the Marco Polo airport:
Bus only: Busitalia ( offers a direct bus from the airport. Take bus line E015 towards Padova Autostazione for 14 stops, get off at Padova Fiera R. The hotel is 181 meters away. The trip is about 65 min and is €8.50.
Bus/Train: Take ATVO ( bus line no. 25a to Venezia P.Roma for 5 stops, get off at Mestre Stazione FS. From there, take a train to Bologna Centrale and get off at Padova stop. Then, take the bus U18 to San Marco for 3 stops, get off at Tommaseo 114. You will find the hotel 130 metres away. It's a 1H 15 min trip and is € 7.50 + 3.40€ + 1,80€.
Taxi: It's a 1H 30 minutes trip and is around 98€.

From Padova train station:
Take the bus U18 to San Marco for 3 stops, get off at Tommaseo 114. You will find the hotel 130 metres away. Ticket (75 min): 1,30€ Ticket (24H): 3,80€

By Car:
The hotel's GPS Coordinates: 45.412671°N 11.892378000000008°E
Parking: Onsite, Indoor and is €10 / day. Parking cannot be reserved in advance


Free, with lunch and coffee provided. Travel, accommodation and breakfast are not included.


You can book a room at Hotel NH Padova from Saturday, April 22nd onwards. Additional lodging suggestions can be found on the 2023 Biocuration Conference website here.

Time Duration Topic Chair Presenters Reporters Group Members
9:00 15 min Welcome Raja Mazumder

Rene Ranzinger

9:15 20 min Glycan Function Overview Mike Tiemeyer


20 min
45 min

Q1. How would your resource extract glycan related data from literature or other sources?

Discussions (All attendees)

Hiren Joshi Yukie Akune

Kristian Axelsen
James Urban

Rene Ranzinger

Cecilia Arighi

Vijay Shanker
10:40 15 min Coffee Break


20 min
45 min

Q2. What type of glycan related data would be useful to your resource, that you don’t currently have access to?

Discussions (All attendees)

Maria Martin Randi Vita

Paul Thomas
Yan Liu

Yasunori Yamamoto

Nathan Edwards

Emily Bordeleau
12:00 60 min Lunch


20 min
45 min

Q3. What type of data, that you do have, might enhance glycan related data?

Discussions (All attendees)

Deepti Jaiswal Kundu Ted Groth

Ten Feizi
Kiyoko F. Aoki-Kinoshita

Frederique Lisacek

Callum Ives

Raja Mazumder


20 min

45 min

Q4. What standards does your resource use for the glycan related annotations?

Discussions (All attendees)

Mike Tiemeyer Adnan Malik

Kalpana Panneerselvam
Susan Bello

Krishna Khakurel

Karina Martinez

Taciana Manso
3:10 50 min Break out session: Chair, presenters, reporters and group members meet with their designated group and prepare a summary/presentation for their question (coffee will be provided)
4:00 60 min 15 min presentations by each group Mike Tiemeyer

Raja Mazumder

Karina Martinez

Rene Ranzinger

Participant Roles
  • Chair - Facilitate discussion sessions
  • Presenters - Give short ~5 minute presentation on their response to discussion question
  • Reporters - Take notes, prepare and present summary for discussion question
  • Group members - Will join chair, presenters & reporters in preparing summary for their question

Presentation/Discussion Sessions

Each presentation/discussion session will focus on one of the four questions above. These sessions will be divided into a presentation section (~20mins) followed by a discussion among all attendees (~45 mins).

For each question, selected resources will give short presentations (~5 mins) on their ideas and strategic thoughts related to how their data of interest can intersect with glycan-related data, including useful annotations, standards, and ontologies. The goal of the discussions will be to improve coordination amongst resources to harmonize and enhance the impact of data related to glycans and glycoconjugates, including structures, functions, biosynthesis, pathophysiology, etc.

One chair will be selected to facilitate each of the presentation/discussion sessions and 2 reporters per question will be responsible for recording and presenting the results during the final session and the Monday Biocuration workshop.

During the summary session at 3:10, each discussion question group (consisting of chair, presenters, reporters and group members) will meet to summarize the findings for their question, and prepare a presentation.

Registered Attendees (Resource/Project)
Resource/Project Attendees
1 GlyGen Karina Martinez, Rene Ranzinger, Vijay Shanker, Nathan Edwards, Mike Tiemeyer, Raja Mazumder, Jeet Vora (remote)
2 Glyco@Expasy Frederique Lisacek
3 Immune Epitope Database and Analysis Project (IEDB) Randi Vita
4 UniProt/iPTMnet/BioCreative Cecilia Arighi
5 GlyCosmos Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto
6 IntAct Kalpana Panneerselvam
7 MGI Susan Bello (remote)
8 UniProt Maria Martin
9 Microarray curation Ten Feizi, Yan Liu, Yukie Akune
10 GlycoShape-3D Callum Ives
11 Hiren Joshi
12 GO/PANTHER Paul Thomas
13 Rhea Kristian Axelsen, Alan Bridge (remote)
14 Glycowork James Urban
15 ELIBIO Project Krishna Khakurel (remote)
16 PRIDE Deepti Jaiswal Kundu
17 GlycoEnzOnto Ted Groth
18 ChEBI Adnan Malik
19 University of British Columbia Emily Bordeleau
20 University of York Jon Agirre (remote)
21 Thomas Lütteke (remote)
22 Glycan microarrays Akul Mehta (remote)
23 IMGT Taciana Manso (remote), Sofia Kossida (remote)
24 O-GlcNAcAtlas Junfeng Ma (remote)
25 PubChem Evan Bolton (remote)
26 VirtualGlycome/SNFG Sriram Neelamegham (remote)

2-Hour Biocuration Workshop (Monday April 24)

Biocuration 2023 will be hosting 5 workshops, including Functional impact of glycans and their curation, at the main conference venue. For additional information, visit the Biocuration website here:


For questions about registration or general inquiries, please contact:
Raja Mazumder:
Karina Martinez:
Jeet Vora: